Re: [Freesurfer] Cortical Thickness Using N30R83 Atlas

-- Ryan Flores Clinical Research Coordinator On 6/14/18, 11:02 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgreve@mgh.harvard.edu> wrote: The --trgsurfval is just the output (ie, lh.atlas.nii.gz sampled onto the surface of the subject). Use nii.gz or mgz for the output (not img). On 06/14/2018 01:46 PM, Ryan Flores wrote: > External Email - Use Caution > > Thank you for your response. Just to clarify, the first command should be mri_vol2surf, correct? It appears to have worked; however, I'm not sure what my --trgsurfval should be? I'm trying the following commands, where mni is the subject directory for the mni brain I recon-ed and sub01 is the subject I want to transfer the atlas to so that I can obtain the cortical thickness. > > 1. mri_vol2surf --mov atlas.nii.gz --regheader mni --hemi lh --projfrac-max 0 1 .1 --o lh.atlas.nii.gz > 2. mri_surf2surf --srcsubject mni --srcsurfval lh.atlas.nii.gz --trgsubject sub01 --trgsurfval hammers-01-lh.img --mapmethod nnf > > I tried running mri_surf2surf --help, but unfortunately the examples didn’t really apply to my case. I apologize for the potential trivial question in advance. Thanks again for your help. > > Best, > > Ryan > -- Ryan Flores Clinical Research Coordinator On 6/14/18, 8:33 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgreve@mgh.harvard.edu> wrote: You can always get info by running the command with --help. mri_vol2vol --mov atlas.nii.gz --regheader subject --hemi lh --projfrac-max 0 1 .1 --o lh.atlas.nii.gz This assumes that the atlas is in registration with the mni152 (you can test with tkregister --mov atlas.nii.gz --s subject --regheader --reg deleteme.dat, the two volumes should be in registration) You can take lh.atlas.nii.gz and use it as input to mri_surf2surf to transfer to an individual. Make sure to use --mapmethod nnf On 06/13/2018 06:59 PM, Ryan Flores wrote: > > External Email - Use Caution > > Hello all, > > I am hoping to obtain structural information (e.g., cortical > thickness, surface area, and volume) based on the n30r83 (aka > Hammersmith) atlas, which is in MNI space. The atlas differentiates > between the hemispheres by using odd/even numbers in the labels. > > After looking through the archives I found a potential solution, which > entails using the mri_vol2surf & mri_surf2surf commands. I’ve recon-ed > the MNI brain to obtain the proper space; however, I’m unsure of how > exactly to implement the commands and which flags are relevant. Any > advice would be greatly appreciated. > > Thank you for your time. I look forward to hearing from you. > > Best, > > Ryan > > -- > > Ryan Flores > > Clinical Research Coordinator > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer